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T-B-F / pyHCA

pyHCA repo @callebautlab
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Biopython Alphabet package has been removed #4

Closed cgpapado closed 3 years ago

cgpapado commented 3 years ago

Due to biopython update the package Alphabet does not exist any more . As a result the script does not work any more and gives the following message:

ImportError: Bio.Alphabet has been removed from Biopython. In many cases, the alphabet can simply be ignored and removed from scripts. In a few cases, you may need to specify the molecule_type as an annotation on a SeqRecord for your script to work correctly. Please see https://biopython.org/wiki/Alphabet for more information.

T-B-F commented 3 years ago

Could you provide me an error line number?

cgpapado commented 3 years ago

I fixed the problem myself to my local version. What I did was:

  1. To delete the line 16: "from Bio.Alphabet import IUPAC"
  2. Replace the line 633: “prot_alphabet = set(IUPAC.protein.letters)” with “ prot_alphabet = ‘ACDEFGHIKLMNPQRSTVWY’ “ in the HCA.py script. After these corrections the program is installed and runs with no problems on my computer!
T-B-F commented 3 years ago

Ok, I fixed it too with a more stable fix which should work with old and new version of biopython

Le mer. 18 nov. 2020 à 18:21, Chris Papadopoulos notifications@github.com a écrit :

I fixed the problem myself to my local version. What I did was:

  1. To delete the line 16: "from Bio.Alphabet import IUPAC"
  2. Replace the line 633: “prot_alphabet = set(IUPAC.protein.letters)” with “ prot_alphabet = ‘ACDEFGHIKLMNPQRSTVWY’ “ in the HCA.py script. After these corrections the program is installed and runs with no problems on my computer!

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T-B-F commented 3 years ago

fixed in 16dee60